Phosphorous fertilization and soil pH affect the growth of deciduous trees in a temperate hardwood forest

To better understand how a forest’s response to P limitation and acidic deposition can change over time, we added P, limestone to raise pH, and a cross-treatment where both P and limestone were added to 3 different northeastern Ohio forest stands over a 12-year period. Internally, we call this experiment APEX, which stands for Acid Precipitation EXperiment. We tracked diameter at breast height (DBH) of the trees annually, conducted foliar nutrient analyses, and collected tree roots to assess treatment impacts on mycorrhizal colonization. We analyzed our dataset in three sections: the first 6 years after manipulation, the latter 6 years, and the entire 12-year period. These sections allowed us to compare differences between early responses to manipulation and later responses. The R code included here shows how these sections of data were analyzed using linear mixed effect models and Tukey post hoc tests (with the R packages lme4 and multcomp, respectively) and graphed (with the package ggplot2). The three R code files include analyses of 1) litter biomass and chemistry (APEX_leaf_litter_R_code.R), 2) ectomycorrhizal (EM) and arbscular mycorrhizal (AM) fungal colonization and root biomass estimates from trees associated with these mycorrhizal types (APEX_mycorrhizal_roots_R_code.R), and 3) relative basal area increment that was calculated for different tree species and mycorrhizal association types using DBH measurements (APEX_RBAI_R_code.R). All input csv files are included here.